I am trying to do tissue separation using QuPath - I tried using pixel classification, and although it was successful in identifying tissue such as muscle, it highlighted areas within other regions. Furthermore, if I tried to separate between tissue regions such as muscularis mucosae and muscularis externa, the classifier would highlight all the muscle regardless of the location. Attaching picture below of example tissue of how I would like the tissue to annotate the regions:
I was suggested using object classifier but it requires information from “Cell detection” function which is not useful in this case (at least in my opinion).
Would anyone have any suggestions on how to go about this?
FYI - the staining is of Picro-Sirius Red for collagen.